I'm trying to make a soartex texture for this mod, but it appears that about half the time the overlay texture is flipped but the underlying ore texture is not.

See here for an example.

Hm, I'm guessing that's because the underlying ore block state doesn't have mirrored variants. You should be able to fix this by overriding the Bedrock Ore mask block state in your resource pack with one that just doesn't contain the mirrored entries.